EPYC

protein-coding

epiphycan, the group of Small leucine rich repeat proteoglycans

Gene summary

Dermatan sulfate proteoglycan 3 is a member of the small leucine-rich repeat proteoglycan family. This gene is composed of seven exons. It regulates fibrillogenesis by interacting with collagen fibrils and other extracellular matrix proteins. [provided by RefSeq, Jul 2008]

Previous symbols:

DSPG3

MANE transcript

NM_004950.5

Inheritance

—

ClinVar variants

U:56B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr12:90,963,682-91,005,026

External References & Databases

Ensembl (ENSG00000083782)

Transcript & Mutation Effects

hg38 • Region Span ~41.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EPYC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004950.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			54 clinvar			54
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar	1 clinvar		3
Total	0	0	56	2	0	58

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004950.5	RefSeq	NP_004941.2	6	MANE Select
ENST00000261172.8	Ensembl	ENSP00000261172.3	6	MANE Select
ENST00000551767.1	Ensembl	ENSP00000448272.1	4	Standard
XM_011538008.2	RefSeq	XP_011536310.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

female pregnancy

Molecular Function

glycosaminoglycan binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261172
Coding exons: 6
Length: 41348
Individuals with no LoFs: 125428
Homozygous LoFs: 2
Heterozygous LoFs: 314
Defined: 125744
p: 0.00126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.264	179	169	1.06	0.00000833	2110
Missense (PolyPhen)		38	39.961	0.95093		513
Synonymous	0.359	61	64.7	0.943	0.00000323	632
Loss of Function	0.701	11	13.8	0.796	8.83e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0019	0.0017	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00042	0.00040	rare
South Asian	0.0077	0.0075	notable
Other	0.00067	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May have a role in bone formation and also in establishing the ordered structure of cartilage through matrix organization.;

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.621
RVIS EVS: 0.51
RVIS percentile EVS: 80.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.179

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium